ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PLXNB3

Gene summary

Gene information	Gene symbol	PLXNB3
	Gene ID	5365
	Gene name	plexin B3
	Synonyms	PLEXB3\|PLEXR\|PLXN6
	Cytomap	Xq28
	Type of gene	protein-coding
	Description	plexin-B3plexin 6
	Modification date	20180523
	UniProtAcc	Q9ULL4
	Context	PubMed: PLXNB3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
PLXNB3	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	16122393
PLXNB3	GO:0007162	negative regulation of cell adhesion	15218527
PLXNB3	GO:0010976	positive regulation of neuron projection development	16122393
PLXNB3	GO:0050918	positive chemotaxis	15218527
PLXNB3	GO:0060326	cell chemotaxis	15218527
PLXNB3	GO:0071526	semaphorin-plexin signaling pathway	15218527

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Exon skipping events across known transcript of Ensembl for PLXNB3 from UCSC genome browser

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Gene isoform structures and expression levels for PLXNB3

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for PLXNB3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_512893	X	153030956:153031035:153031613:153031779:153032327:153033368	153031613:153031779	ENSG00000198753.7	ENST00000538966.1
exon_skip_512901	X	153030956:153031035:153032327:153033368:153033703:153033883	153032327:153033368	ENSG00000198753.7	ENST00000361971.5
exon_skip_512907	X	153030956:153031035:153033703:153033883:153034402:153034531	153033703:153033883	ENSG00000198753.7	ENST00000538776.1
exon_skip_512909	X	153030956:153031035:153033703:153033883:153034616:153034717	153033703:153033883	ENSG00000198753.7	ENST00000538282.1
exon_skip_512917	X	153033703:153033883:153034402:153034531:153034616:153034717	153034402:153034531	ENSG00000198753.7	ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512919	X	153035792:153035901:153035982:153036097:153036212:153036338	153035982:153036097	ENSG00000198753.7	ENST00000538282.1,ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512921	X	153036419:153036536:153036764:153036858:153036940:153037110	153036764:153036858	ENSG00000198753.7	ENST00000538282.1,ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512927	X	153036764:153036858:153036940:153037110:153037318:153037470	153036940:153037110	ENSG00000198753.7	ENST00000538282.1,ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512930	X	153037636:153037742:153038340:153038471:153038684:153038861	153038340:153038471	ENSG00000198753.7	ENST00000538282.1,ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512936	X	153038684:153038861:153038972:153039168:153039313:153039553	153038972:153039168	ENSG00000198753.7	ENST00000538282.1,ENST00000361971.5,ENST00000538776.1,ENST00000538966.1
exon_skip_512944	X	153040755:153040858:153041048:153041115:153041341:153041423	153041048:153041115	ENSG00000198753.7	ENST00000361971.5,ENST00000538776.1,ENST00000482654.1,ENST00000411613.1,ENST00000538966.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PLXNB3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_512893	X	153030956:153031035:153031613:153031779:153032327:153033368	153031613:153031779	ENSG00000198753.7	ENST00000538966.1
exon_skip_512901	X	153030956:153031035:153032327:153033368:153033703:153033883	153032327:153033368	ENSG00000198753.7	ENST00000361971.5
exon_skip_512907	X	153030956:153031035:153033703:153033883:153034402:153034531	153033703:153033883	ENSG00000198753.7	ENST00000538776.1
exon_skip_512909	X	153030956:153031035:153033703:153033883:153034616:153034717	153033703:153033883	ENSG00000198753.7	ENST00000538282.1
exon_skip_512917	X	153033703:153033883:153034402:153034531:153034616:153034717	153034402:153034531	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1
exon_skip_512919	X	153035792:153035901:153035982:153036097:153036212:153036338	153035982:153036097	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000538282.1
exon_skip_512921	X	153036419:153036536:153036764:153036858:153036940:153037110	153036764:153036858	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000538282.1
exon_skip_512927	X	153036764:153036858:153036940:153037110:153037318:153037470	153036940:153037110	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000538282.1
exon_skip_512930	X	153037636:153037742:153038340:153038471:153038684:153038861	153038340:153038471	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000538282.1
exon_skip_512936	X	153038684:153038861:153038972:153039168:153039313:153039553	153038972:153039168	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000538282.1
exon_skip_512944	X	153040755:153040858:153041048:153041115:153041341:153041423	153041048:153041115	ENSG00000198753.7	ENST00000538966.1,ENST00000361971.5,ENST00000538776.1,ENST00000411613.1,ENST00000482654.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for PLXNB3

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000361971	153035982	153036097	Frame-shift
ENST00000361971	153036764	153036858	Frame-shift
ENST00000361971	153036940	153037110	Frame-shift
ENST00000361971	153038340	153038471	Frame-shift
ENST00000361971	153038972	153039168	Frame-shift
ENST00000361971	153041048	153041115	Frame-shift
ENST00000361971	153032327	153033368	In-frame
ENST00000361971	153034402	153034531	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000361971	153035982	153036097	Frame-shift
ENST00000361971	153036764	153036858	Frame-shift
ENST00000361971	153036940	153037110	Frame-shift
ENST00000361971	153038340	153038471	Frame-shift
ENST00000361971	153038972	153039168	Frame-shift
ENST00000361971	153041048	153041115	Frame-shift
ENST00000361971	153032327	153033368	In-frame
ENST00000361971	153034402	153034531	In-frame

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Infer the effects of exon skipping event on protein functional features for PLXNB3

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000361971	6163	1909	153032327	153033368	160	1200	15	362
ENST00000361971	6163	1909	153034402	153034531	1381	1509	422	465

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000361971	6163	1909	153032327	153033368	160	1200	15	362
ENST00000361971	6163	1909	153034402	153034531	1381	1509	422	465

Lost protein functional features of individual exon skipping events in TCGA.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q9ULL4	15	362	1	15	Alternative sequence	ID=VSP_044467;Note=In isoform 2. MCHAAQETPLLHHFM->MELTPASSLTCSLLSPRLPGSFPQLRRVPPCSRPWLPK;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9ULL4	15	362	45	1909	Chain	ID=PRO_0000024674;Note=Plexin-B3
Q9ULL4	15	362	98	107	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	132	140	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	267	370	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	283	315	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	333	357	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	45	471	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	51	51	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	231	231	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	126	126	Natural variant	ID=VAR_050601;Note=A->T;Dbxref=dbSNP:rs34360382
Q9ULL4	15	362	149	149	Sequence conflict	Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULL4	15	362	300	300	Sequence conflict	Note=L->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULL4	15	362	1	44	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	45	1255	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	422	465	45	1909	Chain	ID=PRO_0000024674;Note=Plexin-B3
Q9ULL4	422	465	45	471	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	422	465	45	1255	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

Lost protein functional features of individual exon skipping events in GTEx.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q9ULL4	15	362	1	15	Alternative sequence	ID=VSP_044467;Note=In isoform 2. MCHAAQETPLLHHFM->MELTPASSLTCSLLSPRLPGSFPQLRRVPPCSRPWLPK;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9ULL4	15	362	45	1909	Chain	ID=PRO_0000024674;Note=Plexin-B3
Q9ULL4	15	362	98	107	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	132	140	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	267	370	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	283	315	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	333	357	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	45	471	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	15	362	51	51	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	231	231	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	126	126	Natural variant	ID=VAR_050601;Note=A->T;Dbxref=dbSNP:rs34360382
Q9ULL4	15	362	149	149	Sequence conflict	Note=A->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULL4	15	362	300	300	Sequence conflict	Note=L->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULL4	15	362	1	44	Signal peptide	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	15	362	45	1255	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9ULL4	422	465	45	1909	Chain	ID=PRO_0000024674;Note=Plexin-B3
Q9ULL4	422	465	45	471	Domain	Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00352
Q9ULL4	422	465	45	1255	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for PLXNB3

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A1EG-01	exon_skip_512893	153031614	153031779	153031731	153031731	Frame_Shift_Del	C	-	p.F22fs
LIHC	TCGA-DD-A39Y-01	exon_skip_512893	153031614	153031779	153031731	153031731	Frame_Shift_Del	C	-	p.F22fs
LIHC	TCGA-DD-A3A0-01	exon_skip_512907 exon_skip_512909	153033704	153033883	153033721	153033721	Frame_Shift_Del	C	-	p.Y391fs
LIHC	TCGA-DD-A39Y-01	exon_skip_512907 exon_skip_512909	153033704	153033883	153033817	153033817	Frame_Shift_Del	G	-	p.V423fs
LIHC	TCGA-DD-A1EG-01	exon_skip_512907 exon_skip_512909	153033704	153033883	153033856	153033856	Frame_Shift_Del	G	-	p.L436fs
HNSC	TCGA-CN-5360-01	exon_skip_512917	153034403	153034531	153034499	153034499	Frame_Shift_Del	G	-	p.G455fs
HNSC	TCGA-CN-5360-01	exon_skip_512917	153034403	153034531	153034499	153034499	Frame_Shift_Del	G	-	p.G478fs
LIHC	TCGA-DD-A39Y-01	exon_skip_512927	153036941	153037110	153037068	153037068	Frame_Shift_Del	G	-	p.P848fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_512927	153036941	153037110	153037068	153037068	Frame_Shift_Del	G	-	p.P848fs
CESC	TCGA-LP-A4AV-01	exon_skip_512901	153032328	153033368	153032607	153032607	Nonsense_Mutation	C	T	p.Q132*
SKCM	TCGA-YG-AA3O-06	exon_skip_512921	153036765	153036858	153036783	153036783	Nonsense_Mutation	C	T	p.Q781*
BLCA	TCGA-DK-A3IL-01	exon_skip_512936	153038973	153039168	153038980	153038980	Nonsense_Mutation	C	T	p.R1031*
BLCA	TCGA-DK-A3IL-01	exon_skip_512936	153038973	153039168	153038980	153038980	Nonsense_Mutation	C	T	p.R1054*

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
A204_SOFT_TISSUE	153032328	153033368	153032607	153032607	Missense_Mutation	C	A	p.Q109K
TTC642_SOFT_TISSUE	153032328	153033368	153032607	153032607	Missense_Mutation	C	A	p.Q109K
SKUT1_SOFT_TISSUE	153032328	153033368	153032763	153032763	Missense_Mutation	G	T	p.G161W
JHUEM7_ENDOMETRIUM	153032328	153033368	153032800	153032800	Missense_Mutation	C	T	p.T173M
OC316_OVARY	153032328	153033368	153032860	153032860	Missense_Mutation	C	T	p.A193V
LS411N_LARGE_INTESTINE	153032328	153033368	153032860	153032860	Missense_Mutation	C	T	p.A193V
OC314_OVARY	153032328	153033368	153032860	153032860	Missense_Mutation	C	T	p.A193V
ASPC1_PANCREAS	153032328	153033368	153032898	153032898	Missense_Mutation	C	T	p.R206C
GP2D_LARGE_INTESTINE	153032328	153033368	153032899	153032899	Missense_Mutation	G	A	p.R206H
GP5D_LARGE_INTESTINE	153032328	153033368	153032899	153032899	Missense_Mutation	G	A	p.R206H
SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153032328	153033368	153032937	153032937	Missense_Mutation	C	A	p.L219M
SNUC2A_LARGE_INTESTINE	153032328	153033368	153033030	153033030	Missense_Mutation	C	T	p.R250C
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153032328	153033368	153033069	153033069	Missense_Mutation	G	A	p.V263M
FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153032328	153033368	153033102	153033102	Missense_Mutation	T	A	p.Y274N
NCIH2106_LUNG	153032328	153033368	153033135	153033135	Missense_Mutation	G	A	p.G285S
SNU1_STOMACH	153032328	153033368	153033156	153033156	Missense_Mutation	G	A	p.A292T
DOV13_OVARY	153032328	153033368	153033255	153033255	Missense_Mutation	A	G	p.S325G
LS411N_LARGE_INTESTINE	153032328	153033368	153033271	153033271	Missense_Mutation	G	A	p.R330Q
NCIH1355_LUNG	153032328	153033368	153033298	153033298	Missense_Mutation	G	T	p.R339L
SW872_SOFT_TISSUE	153032328	153033368	153033300	153033300	Missense_Mutation	G	A	p.G340S
D502MG_CENTRAL_NERVOUS_SYSTEM	153032328	153033368	153033327	153033327	Missense_Mutation	G	A	p.V349M
KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153032328	153033368	153033328	153033328	Missense_Mutation	T	A	p.V349E
SNU175_LARGE_INTESTINE	153032328	153033368	153033354	153033354	Missense_Mutation	G	A	p.V358I
SKMEL28_SKIN	153033704	153033883	153033731	153033731	Missense_Mutation	G	A	p.D372N
PA1_OVARY	153035983	153036097	153036039	153036039	Missense_Mutation	A	G	p.H651R
CW2_LARGE_INTESTINE	153035983	153036097	153036087	153036087	Missense_Mutation	G	A	p.S667N
KYSE270_OESOPHAGUS	153036765	153036858	153036787	153036787	Missense_Mutation	G	A	p.R759Q
OCUBM_BREAST	153036941	153037110	153037006	153037006	Missense_Mutation	C	A	p.L805M
YKG1_CENTRAL_NERVOUS_SYSTEM	153036941	153037110	153037009	153037009	Missense_Mutation	G	A	p.G806S
CAL51_BREAST	153038341	153038471	153038408	153038408	Missense_Mutation	G	A	p.R948Q
MOLM16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	153038341	153038471	153038449	153038449	Missense_Mutation	G	A	p.V962M
SW1783_CENTRAL_NERVOUS_SYSTEM	153038341	153038471	153038450	153038450	Missense_Mutation	T	C	p.V962A
D566MG_CENTRAL_NERVOUS_SYSTEM	153038973	153039168	153038988	153038988	Missense_Mutation	C	G	p.I1033M
DBTRG05MG_CENTRAL_NERVOUS_SYSTEM	153038973	153039168	153039025	153039025	Missense_Mutation	C	T	p.P1046S
LC1F_LUNG	153038973	153039168	153039035	153039035	Missense_Mutation	C	T	p.S1049F
IALM_LUNG	153041049	153041115	153041083	153041083	Missense_Mutation	T	A	p.W1457R
NCIH630_LARGE_INTESTINE	153041049	153041115	153041111	153041111	Missense_Mutation	T	A	p.L1466Q
SNU175_LARGE_INTESTINE	153038341	153038471	153038407	153038407	Nonsense_Mutation	C	T	p.R948*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLXNB3

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLXNB3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLXNB3

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RelatedDrugs for PLXNB3

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for PLXNB3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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